This inference to design based upon the appearance of a “purposeful arrangement of parts” is a completely subjective proposition, determined in the eye of each beholder and his/her viewpoint concerning the complexity of a system....which intrigued me. Let's tease out the implications of this quote, and get specific. The fact that something has a function as a consequence of its construction - for example, that a flagellum is able to propel a bacterium - is irrelevant: the idea that the appearance of the arrangement of parts is purposeful is "completely subjective", according to Judge Jones. To the proponent of ID, a flagellum might look purposeful - but, presumably, he thinks, to an opponent of ID, it is just a stalk of protein attached to a cell, with no purpose. And, presumably, because he imagines that to an opponent of ID the flagellum has no purpose, the conclusion of the proponent of ID that it appears designed is subjective and unscientific.
Or let's consider it in connection with the immune system. To the proponent of ID, this appears designed - its function in allowing organisms to deal with infection is what its purposeful arrangement of parts achieve. But to Judge Jones, apparently, this is only subjectively the case - in other words, whilst it might be true for you that the immune system has that function, it needn't be true for somebody else. One wonders what Judge Jones thinks all these funny bits and pieces inside cells and inside multicellular organisms are actually for, if their apparent purpose is a matter of mere subjective interpretation.
The funny thing is that both Darwin and Dawkins were/are happy to accept that biological systems look designed. That was never in dispute. So why does Judge Jones think that the appearance of design is subjective and undermines the case for ID? I would suggest on the basis of this quote that he doesn't really understands ID. Or evolution. Or, to be honest, anything much about cellular biology at all. I'm frankly amazed that opponents of ID set such store by the findings of this judge.